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Oxford nanopore sequencing. If a few problems can be figured out (mainly around machine learning and protein design), then it will beat every other biological detection, diagnosis, and sequencing method by a massive amount (no 10x, but more like 100x-1000x)

It's hard to explain how big nanopore sequencing is if a few (hard) kinks can be figured out. Basically, it has the potential to completely democratize DNA sequencing.

Here is an explanation of the technology - https://www.youtube.com/watch?v=CGWZvHIi3i0






Best part is the Oxford devices are _actually affordable_. Illumina has had such a stranglehold on the market - devices start at around 35k and go up into “this is a house now” territory. Meanwhile the Flongle [0] is $99 and the main Oxford device can be had for $1k.

[0] https://store.nanoporetech.com/us/flowcells/flongle-flow-cel...


> Illumina has had such a stranglehold on the market - devices start at around 35k and go up into “this is a house now” territory.

You cannot effectively sell this kind of device under $25K--support costs simply eat your profit margin.

This is a constant across industries. You either have a $250 thneed (and you ignore your customers) or a $25K thneed (and you have shitty customer support) or a $250K thneed (and you have decent customer support).


Depends what you mean by affordable - low barrier to entry, yes. But bases / $ is still orders of magnitude below where needed to displace Illumina for sequencing of large genomes (eg: human).

Can this be used to make faster corona virus tests ? If so maybe this is the time to Manhattan project this technology.

Generally, yes absolutely. I’ve been doing a project called “NanoSavSeq” (Nanopore Saliva Sequencing) in my free time. It’s published on dat right now since the raw files for Nanopore are really big (got too big for hashbase). There is one company doing it as well, but my version is completely open source and I’ve optimized it for affordable automation.

To give you a sense, you can buy one for 1k and do as much detection as a 64k device, and it’s small enough to fit in a backpack. One device should be able to do 500-1000 tests per 24hrs at a cost of about $10 per test, not including labor.


Is this with multiplexing? Or are you extending the flowcell life?

Multiplexing. I use barcoded primers to amplify the sample, then pool and sequence

Would love to know more. This is fascinating.

The dat website is at dat://aaca379867bff648f454337f36a65c8239f2437538f2a4e0b4b5eb389ea0caff

You can visit with the beaker browser, or share it through dat so it won't ever go down.

You can also visit it at http://www.nanosavseq.com/ (DNS is not up yet, http://167.172.195.83/book/index.html is direct)

It's embarrassingly barren right now, mainly since I've encountered some big problems with getting my DNA quantifier out of storage to start doing a lot more experiments. I'm getting that on Tuesday, so will be updating site then.


The book / documentation is very clean and presented in a fantastic way. May I ask what engine you are using for presenting this book?

mdbook! By the folks making the Rust docs. I love their formatting.

Would you like to work together on this? This is very interesting stuff.

Would love to. Feel free to email me at koeng101<at>gmail.

The Oxford Nanopore people announced that they are in the 'advanced stages' of developing their own Covid-19 test called LamPORE

https://twitter.com/nanopore/status/1263711292868694021

Press release: https://nanoporetech.com/about-us/news/oxford-nanopore-techn...

'Oxford Nanopore is planning to deploy LamPORE for COVID-19 in a regulated setting initially on GridION and soon after on the portable MinION Mk1C.'

The GridION is still expensive and not affordable for a business or private person, a MinION definitely is.


Thanks for those links! I knew it was only a matter of time

There are lots of folks working on LAMP in the DIYbio community. The kinda cool thing is that you can just have a colormetric read-out, so you don't even need Nanopore sequencing. I'm guessing that the reason Nanopore is nice there is to eliminate false positives. I'm more a fan of this approach -

https://www.genomeweb.com/business-news/clear-labs-raises-18...

Because you can recover full genomes as a by-product of diagnostic tests (which is useful for tracing infection, for example https://nextstrain.org/)


Hell yes



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